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Old 09-23-2011, 12:51 AM   #6
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

The default bowtie output will only show mapped sequences. The number of unmapped reads will be reported in the summary provided at the end of the run. You can optionally ask the program to write out a fastq file of the reads which didn't align by passing the --un parameter when you run the program.
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